---
name: "ClonalFrame"
section: "1"
platform: "linux"
package: "clonalframe"
version: "1.2-11+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/ClonalFrame"
---

# ClonalFrame(1)

inference of bacterial microevolution using multilocus sequence data

## NAME

ClonalFrame - inference of bacterial microevolution using multilocus sequence data

## SYNOPSIS

ClonalFrame \[OPTIONS\] inputfile outputfile

## DESCRIPTION

ClonalFrame identifies the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.

Options:

- **-x** NUM

  Sets the number of iterations after burn-in (default is 50000)

- **-y** NUM

  Sets the number of burn-in iterations (default is 50000)

- **-z** NUM

  Sets the number of iterations between samples (default is 100)

- **-e** NUM

  Sets the number of branch-swapping moves per iterations (default is so that half of the time is spent branch-swapping)

- **-m** NUM

  Sets the initial value of theta to NUM (default is Watterson estimate)

- **-d** NUM

  Sets the initial value of delta to NUM (default is 0.001)

- **-n** NUM

  Sets the initial value of nu to NUM (default is 0.01)

- **-r** NUM

  Sets the initial value of R to NUM (default is initial theta/10)

- **-M**

  Do update the value of theta

- **-D**

  Do not update the value of delta

- **-N**

  Do not update the value of nu

- **-R**

  Do not update the value of R

- **-T**

  Do not update the topology

- **-A**

  Do not update the ages of the nodes

- **-G**

  Remove all gaps

- **-H**

  Remove all gaps at non-polymorphic positions

- **-t** NUM

  Indicate which initial tree to use: 0 for a null tree, 1 for a uniformly chosen coalescent tree and 2 for UPGMA tree (default)

- **-w** FILE

  Use Newick file for initial tree

- **-a** NUM

  Sets the first parameter of the beta prior distribution of nu

- **-b** NUM

  Sets the second parameter of the beta prior distribution of nu

- **-U**

  Use uniform priors for rho, theta and delta

- **-B**

  Run in BURST mode

- **-C**

  Run in UPGMA mode with a site-by-site bootstrap procedure

- **-c**

  Run in UPGMA mode with a fragment-by-fragment bootstrap procedure

- **-S** NUM

  Sets the seed for the random number generator to NUM

- **-E** NUM

  Sets the rate of exponential growth (default is 0)

- **-I**

  Ignores first block in the alignment

- **-L**

  Clean-up the alignment before running ClonalFrame

- **-l**

  Minimum distance between two reference sites (default is 50)

- **-v**

  Verbose mode

## AUTHOR

**ClonalFrame** was written by Xavier Didelot.

This manual page was written by Andreas Tille \<tille@debian.org\>, for the Debian project (but may be used by others).